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Yorodumi- PDB-6qw5: Structure and function of the toscana virus cap snatching endonuclease -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qw5 | ||||||
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Title | Structure and function of the toscana virus cap snatching endonuclease | ||||||
Components | RNA-dependent RNA polymerase | ||||||
Keywords | HYDROLASE / Cap snatching endonuclease of Toscana virus at the N-term of the L protein. | ||||||
Function / homology | Function and homology information RNA-templated viral transcription / nucleoside binding / negative stranded viral RNA replication / host cell endoplasmic reticulum / endoplasmic reticulum-Golgi intermediate compartment / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity ...RNA-templated viral transcription / nucleoside binding / negative stranded viral RNA replication / host cell endoplasmic reticulum / endoplasmic reticulum-Golgi intermediate compartment / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / metal ion binding Similarity search - Function | ||||||
Biological species | Toscana virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.988 Å | ||||||
Authors | Reguera, J. / Jones, R. / Bragagniolo, G. / Lessoued, S. / Mate, M. | ||||||
Funding support | France, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structure and function of the Toscana virus cap-snatching endonuclease. Authors: Jones, R. / Lessoued, S. / Meier, K. / Devignot, S. / Barata-Garcia, S. / Mate, M. / Bragagnolo, G. / Weber, F. / Rosenthal, M. / Reguera, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qw5.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qw5.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 6qw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/6qw5 ftp://data.pdbj.org/pub/pdb/validation_reports/qw/6qw5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23892.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 2,4-dioxo-4-phenylbutanoic acid / Source: (gene. exp.) Toscana virus Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: S4ZA26, UniProt: P37800*PLUS #2: Chemical | ChemComp-MN / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.42 % / Description: Thick plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0,1M Hepes pH 7,5 0,75 M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→47.1 Å / Num. all: 44372 / Num. obs: 36170 / % possible obs: 99 % / Redundancy: 10.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.056 / Rrim(I) all: 0.185 / Net I/σ(I): 0.1 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6019 / CC1/2: 0.818 / Rpim(I) all: 0.376 / Rrim(I) all: 0.871 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.988→47.099 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.988→47.099 Å
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Refine LS restraints |
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LS refinement shell |
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